RMSD Matrix calculation module

Submodules

Module contents

RMSD matrix module.

This module calculates of the RMSD matrix between all the models generated in the previous step.

As all the pairwise RMSD calculations are independent, the module distributes them over all the available cores in an optimal way.

Once created, the RMSD matrix is saved in text form in the current rmsdmatrix folder. The path to this file is then shared with the following step of the workflow by means of the json file rmsd_matrix.json.

The module accepts two parameters in input, namely:

  • max_models (default = 10000)

  • resdic_ : an expandable parameter to specify which residues must be considered for the alignment and the RMSD calculation. If there are two proteins denoted by chain IDs A and B, then the user can operate such selection in the following way inside the configuration file

>>> resdic_A = [1,2,3,4]
>>> resdic_B = [2,3,4]

thus telling the module to consider residues from 1 to 4 of chain A and from 2 to 4 of chain B for the alignment and RMSD calculation.

class haddock.modules.analysis.rmsdmatrix.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/analysis/rmsdmatrix/defaults.yaml'))[source]

Bases: BaseHaddockModule

HADDOCK3 module for clustering with RMSD.

classmethod confirm_installation() → None[source]

Confirm if fast-rmsdmatrix is installed and available.

name: str = 'rmsdmatrix'
update_params(*args: Any, **kwargs: Any) → None[source]

Update parameters.

Default Parameters

Easy

allatoms

default: False
type: boolean
title: Atoms to be considered during the analysis.
short description: Atoms to be considered during the analysis.
long description: Atoms to be considered during the analysis. If false (default), only backbone atoms will be considered, otherwise all the heavy-atoms.
group: analysis
explevel: easy

atom_similarity

default: 90.0
type: float
title: Required atom similarity
min: 10.0
max: 100.0
short description: Required similarity (in %) between the number of atoms in the input models.
long description: Required similarity (in %) between the number of atoms in the input models. If the similarity is higher than this value, the RMSD calculation is performed on the common atoms. Otherwise, the calculation is stopped. The lower the value the looser the checks.
group: analysis
explevel: easy

max_models

default: 10000
type: integer
title: Maximum number of models to calculate RMSD matrix
min: 1
max: 20000
short description: If the number of models exceeds max_models the execution is blocked
long description: If the number of models exceeds the few thousands, the calculation of the RMSD matrix is computationally demanding, especially in terms of CPU and disk space.
group: analysis
explevel: easy

resdic

default: []
type: list
title: List of residues
short description: The residue numbers that should be used in the alignment and in the RMSD calculation.
long description: resdic_* is an expandable parameter. You can provide resdic_A, resdic_B, resdic_C, etc, where the last capital letter is the chain identifier.
group: analysis
explevel: easy